I am new to Dipy and this email list. I am working on post-processing streamlines created with the Tractoflow pipeline. The pipeline’s final output is a whole brain tractogram .trk file created with Dipy code. As a next step, I would like to separate the whole brain tractogram into different white matter bundles, particularly the 80 bundles included in bundle_atlas_hcp482. Ultimately, I would like to use these extracted bundles to produce the AFQ-like tract profiles.

Since I am trying to script as much of this as possible, I would like to use the command line version of RecoBundles (dipy_recobundles). I have three questions about running this command.

1) dipy_recobundles takes as required inputs a whole brain tractogram and one .trk model file. Is it possible to, without looping the command, segment the whole brain tractogram with all of the atlas bundles?

2) The RecoBundles tutorial listed on the Dipy website includes a registration step to make sure the target and model brains are in the same space. Is this step included in the command-line version, and if not is there a command that will do this (I also have the whole brain model from the hcp482 atlas for this purpose)?

3) Am I using the right command to do what I described in the first paragraph? I am not sure I understand the difference between dipy_recobundles and dipy_labelsbundles.

I am running the latest version of Dipy (1.1.1) from the Brainlife docker container on a linux HPC. I would be happy to provide more information as needed.

Thank you,

Steven

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